Toxoplasma gondii is the most successful protozoan parasite that infects a variety of animal hosts and humans worldwide. It has been recognized as the major food- and water-borne pathogen in humans due to frequent outbreaks of infections. One-third of the human population worldwide is chronically infected. Infections in healthy pregnant women may cause blindness, mental retardation, or even death of the fetus. Reactivation of latent infection In immunocompromised patients such as AIDS can cause life-threatening encephalitis. Recently, 62 globally diverse T. gondii strains have been sequenced. Comparative genome analysis has revealed that tandem amplification and diversification of secretory pathogenesis determinants (SPD) is the primary feature that distinguishes T. gondii from its closely related genomes of coccidian parasites such as Hammondia hammondi, Neospora caninum, and Sarcocystis neorona. In addition, the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are enriched in tandemly clustered SPD. The difference in distribution of SPDs among T. gondii clades may influence the parasite's transmission, host range, and pathogenicity. To take full advantage of these genomic data and develop hypothesis-based research, it is necessary to train scientists on how to explore these data. Given that T. gondii is an important parasite infecting more than half the human population in South America, and that a significant number of T. gondii strains sequenced were collected by our collaborators in that region, we propose to organize a Workshop on Apicomplexan Genome Analysis in Brazil. We expect this effort will let scientists in the field to make good use of the whole genome sequence data to study the biology of T. gondii and related protozoan parasites. In addition, this effort will also strenthen our ongoing collaboration and lead to more long-term collaboration in South America. The proposed workshop will be held in the Department of Preventive Veterinary Medicine at the University of So Paulo, Brazil. The workshop will be open to scientists in South America and it will last for 5 days, from September 26-30, 2016. We expect to train 20 undergraduate students, graduate students, postdoctoral fellows, and young faculty in this workshop. The objectives of the workshop include: 1) To learn how to retrieve and manipulate different kinds of omics sequencing data (sequencing reads, SNPs, genome assemblies, RNAseq reads, annotation data, etc.) from public DBs including EuPathDB and GenBank; 2) Mapping sequencing reads to reference genomes and SNP identification; 3) SNP annotation (finding what SNPs generate frame shifts, missense mutations, etc); 4) Building SNP-based phylogenetic networks for Toxoplasma classification; and 5) RNAseq and gene enrichment analyses.